14-52313933-C-G

Position:

• chr14-52313933-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000691625.2(ENSG00000289424):​n.167G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 152,168 control chromosomes in the GnomAD database, including 2,422 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.15 (2422 hom., cov: 32)
• Consequence: ENSG00000289424 ENST00000691625.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.669

Genes affected

ENSG00000289424 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.441 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.52313933C>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000289424	ENST00000691625.2	n.167G>C		non_coding_transcript_exon_variant	1/4

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22934 AN: 152050 Hom.: 2423 Cov.: 32

Gnomad AFR AF: 0.0968

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.408

Gnomad SAS AF: 0.458

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.162

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.151 AC: 22937 AN: 152168 Hom.: 2422 Cov.: 32 AF XY: 0.162 AC XY: 12027 AN XY: 74374

Gnomad4 AFR AF: 0.0965

Gnomad4 AMR AF: 0.264

Gnomad4 ASJ AF: 0.136

Gnomad4 EAS AF: 0.409

Gnomad4 SAS AF: 0.457

Gnomad4 FIN AF: 0.120

Gnomad4 NFE AF: 0.123

Gnomad4 OTH AF: 0.165

Alfa AF: 0.132 Hom.: 204

Bravo AF: 0.154

Asia WGS AF: 0.354 AC: 1234 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	5.1
DANN	Benign	0.57

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2075797; hg19: chr14-52780651;